Coming Home
by MrRigger
Summary: After the fight at the Valley of the End, Naruto is taken by Itachi. Three years later, he's back. How have things changed? What happened to Akatsuki?


**This was a rather rabid plotbunny that I needed to write down. It was written rather hastily, and I checked for the most part, but I only went so far. I hope you enjoy. Also, this is very AU. Keep that in mind. I don't support insanely strong Uchiha's, and you should be able to see where I'm coming from with this fic. Don't flame me about not staying true to canon, the only thing different is apparent, and purposeful.**

* * *

Kakashi burst through the tree line and entered the Valley of the End. Pakkun had tracked his two students to here, and it was the last place Naruto and Sasuke could do battle before crossing into Sound territory. The copy-nin wasn't sure, but he was almost certain this would be the place of their final showdown.

But as he surveyed the battlefield, he found it was empty. Signs of a fierce battle were quite apparent, but the combatants were nowhere to be seen.

"They were both here," Pakkun said. "Sasuke left before Naruto. Two others took Naruto away. With the rain, I won't be able to track them any further. Sorry Kakashi." Nodding his had, Pakkun poofed out of sight.

Kakashi searched the valley for a few more minutes, but didn't find anything. Not that he expected to. Pakkun was his best tracker, and if he couldn't find him, chances were that he couldn't either. With a sorrowful heart, the elite jounin turned and started back for Konoha.

--

"What do you mean you can't find them?!" Tsunade demanded. Kakashi had just told her about Naruto disappearing.

"The rain washed away the scent trails, and there was no other way I could track them. Sasuke had likely already crossed over into Sound's territory, and I couldn't find any trace of Naruto leaving. Pakkun said there were two other scents who picked him up, but he didn't know who they were. Being that there was two of them, and I couldn't find any race of them other than that, I assume you can figure out my theory."

"Akatsuki," she whispered, the word laced with killing intent. Kakashi shuddered. Even though he knew the blonde Hokage wasn't mad at him, he also knew he wasn't safe from her wrath.

"That's what I believe," Kakashi confirmed.

Jiraiya, who had been sitting quietly in the corner, through the whole meeting, spoke up. "I'll speak to my contacts. If they know anything, I'll get it back to you as soon as possible. But I don't understand why they would capture him now. My contacts said they wouldn't be ready to move for another three years. If they aren't ready to extract the Biju, why would they capture Naruto?" The trio sat silent for a minute or two, until Jiraiya brightened. The perverted author bite his thumb and ran through five familiar handseals. A poof of smoke later, and Gamakichi sat on Tsunade's desk.

"Hey, what'dya need? And do you have any sweets? I don't do this for free you know."

Jiraiya rolled his eyes and tossed the toad a piece of candy. No one wanted to know where he got it. "I know a summon can detect when a summoner dies. Naruto's disappeared. Can you tell if he's still alive?"

Gamakichi closed his eyes and concentrated. His father had just recently started teaching him how to do this. "Yeah, he's alive. What happened to nii-san?"

Jiraiya took a deep breath, as if decided whether or not to tell the summon animal. "We believe he's been taken by Akatsuki. We wanted to know if there was still anything left to save."

Gamakichi was suddenly depressed. He actually liked Naruto, and was looking forward to seeing the blonde grow up. "Alright. I've got to go tell this to pop. If nii-san summons any of us, we'll tell you as soon as we can."

Gamakichi poofed out, leaving the trio to drink themselves into oblivion.

--

Tsunade stood before the council. The Konoha council was made up of the council of elders, the council of shinobi, and the civilian council. The council of elders was currently made up of Sarutobi's former teammates, Koharu and Homura, and the head of ANBU, Danzo. The council of shinobi was made up of the heads of the most powerful clans in the village. The civilian council was mostly people who had a lot of money and influential merchants. Tsunade thought the council as a whole had only a few brain cells and usually left them at home.

"Where's Uchiha Sasuke? I know you sent off a rescue mission after he had been kidnapped by Orochimaru's ninja, why isn't he back yet?"

Tsunade gritted her teeth. "He wasn't kidnapped, he abandoned the village. He's a missing-nin. Get that through your head. And as for why he's not been captured, it's because you keep sending out my shinobi in order to keep up the idea that we're stronger than we really are. If you let me send them where they're really needed, we would be stronger!"

The merchant narrowed his eyes. "You should remember who you're talking to."

Tsunade released a focused blast of killing intent. "You should remember you're talking to someone who can kill you before you can blink," she spat.

The merchant paled and didn't respond.

"Who did you send after Sasuke?" Koharu asked.

"Since you keep taking my more experienced nin, I had to send a new chuunin and a handful of genin after the traitor."

"Who did you send, Hokage-sama?" Koharu demanded.

"Nara Shikamaru, Akimichi Chouji, Inuzuka Kiba, Hyuuga Neji, and Uzumaki Naruto. Rock Lee and the Suna-nin Gaara, Temari, and Kankuro all joined after they left."

Cries of protest went up as the council registered whom Tsunade had sent out. After thirty seconds, Tsunade punched the desk in front of her, and obliterated it. The council silenced immediately.

"According to Hatake Kakashi, Uchiha Sasuke and Uzumaki Naruto battled at the Valley of the End. Uchiha Sasuke won, and ran off to join Orochimaru. Shortly after, two as of now unidentified people abducted Naruto. We believe them to members of Akatsuki, as Kakashi couldn't find any trace of them other than their scent, which disappeared quickly."

Tsunade's eyes grew grave. "If Akatsuki has their hands on Naruto, we just got a lot more problems. He's likely already dead." As far as she knew, the council didn't know about Naruto's contract with the toads, and she was perfectly happy keeping that way.

The meeting lasted a while longer, with lots of discussion and really nothing being accomplished. Sasuke was eventually declared a B-class missing-nin, and no decision was made about Naruto.

--

Three Years Later…

--

A black-cloaked trio walked towards the west gate of Konoha. The chuunin guards had been having a rather boring day. Of course, guard duty was always rather boring. It was the preferred sakes in the weekly chuunin poker game. The more you lose, the more guard duty you have.

The head chuunin on duty confirmed their papers as being independent bounty hunters, with the explanation that they wanted to discuss payment on some missing-nin they had taken out. The chuunin waved them through lazily, going back to his post, where he could hopefully get some more reading done before someone interrupted him. For a job where nothing happened, he sure seemed to be bugged constantly.

"Konoha's guards are even more lax now than they were three years ago," the tallest one commented once they were out of hearing range. "Didn't even have to put them in a genjutsu this time."

"Oh stuff it, fishface. We'll fix it later. Let's just get to where we need to be right now."

--

In the Hokage's office, a familiar trio was drinking. Tsunade had escaped Shizune's badgering for the moment, Kakashi didn't have a mission, and Jiraiya was simply being Jiraiya.

"Three years since he disappeared. I still don't understand why he's still alive if Akatsuki has him. But every message from Gamakichi says that Naruto's fine, and will come back when he can. I don't understand," Jiraiya mumbled around his saucer of sake.

"Well, Naruto has always been a little off," Kakashi mentioned offhandedly. "During his genin test, instead of hiding, he ran straight for me. You know, if they had been a team for a long time, and actually knew how to work together, that would have been a great distraction for one of the others to rush in and grab a bell. Oh well."

"A little off? You don't know the half of it. Kid took on an enemy on elite jounin level after I was paralyzed and nearly beat him on his own," Tsunade threw in. Sounds of a scuffle outside caught their attention.

"Let us in before I have to hang you naked from the Hokage monument, you stupid bastard!" a voice proclaimed. Kakashi, the closest of the three, was nominated to go check out what was going on. As soon as he cracked the door, it was flung the rest of the way as a black-cloaked figure dashed into the room faster than Kakashi could react.

"Jeez, just as hard as ever to get in here. You should get nicer guards, you know that Baa-chan?"

Tsunade sobered up immediately at the name. "Only one person has the right to call me that, and you're not him. Now tell me who you are before I kill you."

The black-cloaked figure was quickly flanked by his two companions. The center figure tossed back his hood and revealed his identity. "Hiya Baa-chan, Ero-sennin, Kakashi-sensei."

"N-naruto?" they stammered as one.

"Yep! I'm back, and I brought friends." The two flanking him slid their hoods down as well, revealing Uchiha Itachi and Hoshigaki Kisame.

"Uh, you do realize you're standing between two of the most wanted men in the ninja world, right?" Jiraiya asked.

"You're telling me," Naruto said. "Once, we got caught in a festival and Itachi was mobbed by fangirls. I swear, they're more dangerous than fighting the Kyuubi!"

Kakashi nodded knowingly, he had had his fair share of fangirls in his younger years. The only reason they weren't around any longer was because he hadn't shown his face in public in years.

"That's not what I mean, and you know it," Jiraiya ground out. "So what are you doing with them?"

Naruto shrugged. "They're my friends. And when they're not trying to kill me, they're pretty nice guys."

"Where have you been for the past three years?" Tsunade asked, apparently just now getting her voice back from seeing one of the only people she truly cares about again.

Naruto walked over to one of the chairs and plopped down. He wasn't going to stand up for this story. "Well, I was fighting Sasuke at the Valley of the End, when it came down to one final clash. **Chidori** versus **Rasengan**. Unlike him, I was going to incapacitate him instead of killing him. I would have won too, if I hadn't cared about bringing him back, too. But after he left me for dead to go join the hebi-teme, Itachi and Kisame here picked me up. They ended up taking me to Akatsuki headquarters, and I was pretty freaked out a first too. Once they got me to understand that they weren't going to kill me right away, I calmed down some. They had to wait three years before they could seal any more Biju, so I was safe until then. Until then, Itachi convinced the rest of Akatsuki to train me until they could seal me away, you know? The thing that convinced them was, 'who better to track down jinchuuriki than one of their own?' It actually kind of makes sense, but whatever. I'm betting you want to know why I'm here and not either tracking down other Biju or being sucked into a statue, aren't you?"

"Yes, that would be one thing I want to know," Tsunade said through gritted teeth.

"Well, Itachi and Kisame found out what Akatsuki was really after, and they didn't want any parts of it, but they knew they couldn't take down the rest of the group themselves, so they needed someone who could get strong enough to help them escape."

"What was Akatsuki's true intentions?" Jiraiya asked seriously.

"I'm getting to that, just chill out," Naruto admonished. "So anyway, they picked me up, and for the past three years, I've been trained to help take down Akatsuki, and now that I have, I'm back."

Kakashi shook his head. "You mean to tell me that you helped take down some of the most powerful nin in the world? Naruto, not to disagree, but even with three years of solid training, I still don't think that's possible. Even with as long as I've trained, I couldn't handle fighting just Itachi when he came after you three years ago. What makes you think we would believe you're able to take down all of them?"

Itachi spoke this time, coldly. "Surely you're joking, Kakashi. If you ever took time to look at your students, you would see Naruto had potential far surpassing anything Konoha has ever seen."

"What are you talking about?"

Itachi narrowed his eyes. "Look at it logically. In the academy, Naruto was sabotaged by his instructors. Only one of them had the intelligence to see that the boy they were teaching wasn't the fox, and he could only do so much. Moving on to his graduation, Naruto was able to sneak into the Hokage Tower undetected, steal the Forbidden Scroll out from under the Hokage's nose, and learn a jounin level technique in a matter of hours, with absolutely no outside instruction. And I've seen the instructions for that technique in the scroll, remember? They aren't that detailed. He shouldn't have been able to figure it out unless he was a prodigy among prodigies."

"When he was placed on a genin team, he was stuck with an instructor that didn't teach him anything."

Kakashi spoke out against that. "I resent that. I did teach him, perhaps not as much as I should have, but you can't say something like that."

Itachi continued. "Very well, you taught Naruto basic tree climbing, only after being attacked by an A-class missing-nin, and you gave him hardly any more instruction than he would be able to find on a scroll. You gave him a demonstration, then told him to figure it out. It probably would have been better if you just gave him a scroll. It would have been more efficient.

"After beating an opponent the prodigy of the team, Sasuke, couldn't beat, you continued to ignore him. Don't lie Kakashi, we've had spies tracking Naruto for a long time. We know all this information is accurate.

"During the chuunin exams, Naruto had a **Gogyo Fuuin**, placed on him, sealing off most of his chakra and absolutely destroying his chakra control. He still beat Inuzuka Kiba, someone who was far favored to win the match. The seal that was placed on him, that you didn't even notice because you were too wrapped up in working on my brother, wasn't removed until much later. When Naruto asked you to help him train for the finals, you refused. You gave Naruto a teacher he didn't respect, and left him on his own once again.

"Before I go on, Kakashi, what were you thinking when you decided to train Sasuke? Orochimaru's curse seals are well documented in their effects. Primarily, they increase the victim's lust for power. By giving him specialized training, and your own personal jutsu, you were just increasing the effect the seal would have on him.

"Ebisu, despite being one of the best teachers in the village, could barely do more than show Naruto the basics of water walking before Jiraiya knocked him out. Jiraiya, you hardly did better than Kakashi to start with. You showed Naruto the exercise, and left him to figure it out on his own. If he weren't the prodigy he is, he would never have finished it as fast as he did. Yes, you did allow him to sign the toad contract, but you didn't give him any real instruction on how to do it.

"In the finals, Naruto faced Hyuuga Neji, someone hailed as the strongest **Byakugan** user in a century. Naruto had no instruction on how to beat a Hyuuga, not even a scroll containing their basic capabilities, and he still won. He was hit with the Hyuuga's special attack, had all his chakra cut off, and still won. Not long after having his chakra cut off, Naruto summoned Gamabunta, and defeated a fully released Ichibi no Shukaku. Sasuke, the one you continued to praise, Kakashi, couldn't touch Gaara even partially released, with the curse seal active and boosting his abilities.

"Jiraiya, during the time you took him to find our lovely Hokage, you started teaching Naruto the **Rasengan**. It took the Yondaime-sama three years to create it, and it took you six months to get it, even with Yondaime-sama helping you closely. You told Naruto the basic steps, gave him a few hints here and there, and Naruto had it in a month.

"During the fight with Orochimaru, Naruto took down an opponent on the level of elite jounin after training himself to point of exhaustion seven days straight.

"After traveling from Konoha to the edge of Fire Country in under two days, surviving the initial attacks of each of the Sound Four, fighting Kimimaro, someone Orochimaru would have feared if not for his unnerving loyalty, Naruto finally caught up with Sasuke. Exhausted, he fought a fresh opponent. Naruto was fighting to capture, Sasuke was fighting to kill. Sasuke _barely_ won.

"So tell me, Kakashi, after understanding all that he's done, without any instruction further than what he could find in scrolls, why is it so hard to believe that Naruto could advance as far as we said? Especially since he had training from the most dangerous people in the business."

Tsunade, Jiraiya, and Kakashi were all red-faced after hearing how they had overlooked Naruto's potential. "Well, when you put it like that…" Kakashi trailed off.

"Precisely."

After a moment of uncomfortable silence, Tsunade cleared her throat. "So, does this mean all the rest of Akatsuki is dead?"

Naruto gave a foxy grin and pulled out a bunch of storage scrolls. As he talked, he unsealed them. "Zetsu of the Grass. Taught me spying, information gathering, and survival skills. Though he did try to eat me a couple of times. Deidara of the Rock, my demolition and strategy instructor. I actually didn't want to kill him, but when he tried to kill me, I didn't have a whole lot of a choice. Sasori of the Sand, taught me puppetry, poisons, and tactics. I didn't really want to kill him either. Kakuzu of the Waterfall, he taught me taijutsu and elemental manipulation, as well as some ninjutsu. Hidan of the…well, I never really figured out where he came from. He always freaked me out. But you wouldn't believe what I had to do to kill him. We cut off his head and burned his body, and he still wouldn't stop talking! He really died about two weeks ago, and I killed him long before that."

Naruto looked back at the two S-class criminals behind him. "Of course, Itachi and Kisame taught me a lot too. I went to Wave and got Zabuza's sword, and learned kenjutsu with that. And Itachi taught me loads of ninjutsu."

Jiraiya spoke up now. "I hate to tell you kid, but that's not all the Akatsuki members. And you still haven't told us what they really wanted!"

Naruto waved his hand. "I'm getting to it. Now, the final three were the most important. They liked to make everyone believe they were human, but they weren't. They were demons, demons that Kyuubi recognized. Pein, the leader, was a demon on the cusp of becoming a Greater Demon, a Biju. The only way for a demon to ascend to that state is to defeat one of the current Biju in one on one battle. Pein went after Kyuubi, and when he lost, Kyuubi banned Pein from the demon realm, and trapped him here in a human body. Pein took his two underlings with him, who took the names of Tobi, and Konan. They were the hardest to kill, but I did it. Now, I expect some serious money for these bounties. And don't try to cheat me! Kakuzu taught me all about money management."

"But what did Akatsuki what!!!" Jiraiya was close to tearing his hair out.

"The human members wanted to rule the world, while Pein, Tobi, and Konan were planning on taking their revenge on the Biju and using their chakra to tear a whole into the demon realm so they can go home."

Kisame's frank declaration of what Akatsuki wanted floored the people who didn't know. After they absorbed that knowledge, Tsunade took the conversation down a different route.

"Why did you two help Naruto?"

Kisame shrugged. "We both just joined Akatsuki for the protection it offered. We weren't really looking to rule the world."

Kakashi asked something that he had long wanted to know. "Itachi, why did you slaughter your family?"

Itachi glared at him, leaking killing intent. "I did not slaughter my family, I executed them. They were planning a coup, and wanted to rule Konoha for themselves. I wouldn't have been believed if I went to the council, so I took matters into my own hands. After that, it was just easier to go missing than justify my actions to people who wouldn't listen anyway. As for Sasuke, I didn't believe he would ever listen to the advice of the person who killed his family, so I gave him some bad advice. It's not my fault the kid's always been fucked up in the head."

"As for me, the Kiri leaders decided I was getting too powerful for my own good," Kisame explained. "Sure, I killed them, but they tried to kill me first."

"We still have to go down to Suna and collect the bounties on our former teammates from there, but we'll probably be back soon," Naruto said after the six discussed a payment plan for the massive bounty Naruto was getting over sake. "If we aren't back soon, I've either decided to visit with Gaara for a while, or we've just gone straight on to Oto. We still need to kill Orochimaru and Kabuto."

"What about Sasuke?" Kakashi asked.

"What about him? If you give me your word that the bastard will be executed once I bring him back, I'll do it. If not, he can stay missing for all I care."

Tsunade gave her word that Sasuke wouldn't be saved by the council, whose power had decreased greatly in the three years Naruto had been gone, and Naruto had one more question.

"Are we going to be welcomed back as Konoha Shinobi? I mean, if we aren't, I'll drop off Sasgay and figure something else out."

Tsunade sighed. "That, I don't know. A lot power the council had over me left when you were kidnapped three years ago, because they could no longer threaten to execute you. Now that you're back, I don't know what's going to happen."

Naruto nodded. "Alright, I'll go kill Orochimaru and Kabuto, bring back Sasuke, and hide after that. Get me a message through Gamakichi as to what the council wants to do with me, and I'll base my decision off that."

After Naruto, Itachi, and Kisame disappeared, Tsunade collapsed into her chair. "Did anyone else notice that Naruto is probably the most powerful person in the world now?"

Kakashi nodded, and Jiraiya shrugged. "Someone has to be the strongest. I'm just glad it's someone who doesn't want to kill me."

--

Five Years Later…

--

"Ahhh, it's good to be the Kage," Naruto sighed as he lounged in the personal onsen of the Otokage. The Konoha council had rejected allowing Naruto to join their ranks once more, and wanted to mark him as a missing-nin, but Tsunade didn't allow them to do that. If they weren't going to allow him back in, they couldn't mark him.

Sasuke was executed, much to the dismay of the council. They had planned on saving him as soon as he got back in the village, but Tsunade got there first. She disbanded the council soon after, on charges of treason and undermining the Hokage's authority.

Itachi and Kisame joined Naruto in Oto, as his personal guards. He still treated them like friends, and they taught him what they could from their areas of expertise. Itachi met a civilian who he fell in love with and began to restore the Uchiha clan. So far, he had twin daughters and a son who had more energy than Naruto. Kisame, still single, laughs at him daily when he sees him chasing his kids and failing to catch them.

Naruto built Otogakure into one of the strongest villages in the world. He managed to arrange peace treaties with all the villages except Konoha, and even had a non-aggression pact with them. He eventually married Temari as a way to seal the pact between Suna and Oto, and couldn't be happier. Neither could Gaara. He didn't trust anyone else with his sister. Temari was currently expecting their first child, and Naruto had the lumps from her mood swings to prove it.

"Yes, it's definitely good to be the Kage."


End file.
